Short- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa

Fiona B. Tamburini, Dylan Maghini, Ovokeraye H. Oduaran, Ryan Brewster, Michaella R. Hulley, Venesa Sahibdeen, Shane A. Norris, Stephen Tollman, Kathleen Kahn, Ryan G. Wagner, Alisha N. Wade, Floidy Wafawanaka, F. Xavier Gómez-Olivé, Rhian Twine, Zané Lombard, Scott Hazelhurst () and Ami S. Bhatt ()
Additional contact information
Fiona B. Tamburini: Stanford University
Dylan Maghini: Stanford University
Ovokeraye H. Oduaran: University of the Witwatersrand
Ryan Brewster: Stanford University
Michaella R. Hulley: University of the Witwatersrand
Venesa Sahibdeen: National Health Laboratory Service & University of the Witwatersrand
Shane A. Norris: University of the Witwatersrand
Stephen Tollman: University of the Witwatersrand
Kathleen Kahn: University of the Witwatersrand
Ryan G. Wagner: University of the Witwatersrand
Alisha N. Wade: University of the Witwatersrand
Floidy Wafawanaka: University of the Witwatersrand
F. Xavier Gómez-Olivé: University of the Witwatersrand
Rhian Twine: University of the Witwatersrand
Zané Lombard: National Health Laboratory Service & University of the Witwatersrand
Scott Hazelhurst: University of the Witwatersrand
Ami S. Bhatt: Stanford University

Nature Communications, 2022, vol. 13, issue 1, 1-18

Abstract: Abstract Human gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world’s population. Here, we evaluate gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyze stool from adult females living in rural Bushbuckridge (n = 118) or urban Soweto (n = 51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterizing microbiomes of individuals living outside high-income countries, yielding artificially low beta diversity measurements, and generate complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas. Our results suggest that the gut microbiome of South Africans does not conform to a simple “western-nonwestern” axis and contains undescribed microbial diversity.

Date: 2022
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DOI: 10.1038/s41467-021-27917-x

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